Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.

ABSTRACT:

Background

Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts.

Methods

We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest) of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones r

SUBMITTER: Gupta S 

PROVIDER: S-EPMC521684 | biostudies-literature | 2004 Sep

REPOSITORIES: biostudies-literature